User:Tommie Hata/Protein Structure Tutorial



Lysozyme, PDB ID 2lyz

Amino acids and primary structure

Proteins are polymers of amino acids. The "backbone" of the protein is made up of carbons and nitrogens. The amino acid sidechain extends out of the backbone. Here, the backbone is colored in CPK coloring and the sidechains are colored green. The linear sequence of amino acids in a polypeptide is referred to as its "primary structure".

Interactions between the protein backbone: secondary structure

Hydrogen bonds between backbone amide and carboxyl groups maintain some local structural characteristics referred to as secondary structure. Two common types of secondary structure are the alpha helices and the beta pleated sheet. Here, alpha helices are colored red and beta pleated sheets colored blue in a "ribbons" display.

3D structure of a protein maintained by interactions between amino acid sidechains: tertiary structure

The overall shape of a protein is maintained by the interaction between amino acid sidechains. The distribution of these sidechains across the protein (the primary structure) is largely responsible for determining tertiary structure.

Types of tertiary interactions

Nonpolar sidechains and the hydrophobic core.

Charged sidechains and ionic interactions.

Ionic Interactions with surface.

Polar and charged sidechains.

Cysteines and disulfide bond formation in oxidizing environments.

SS bond shown between alpha carbons in backbone view.

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